Quick Glimpse

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Cover Image

We use snakemake [@Dadasnake2021] to maintain reproducibility and improvement of the bioinformatics analysis of microbiome data.

Microbial Profiling Options

Classification of Operational Taxonomic Units (OTUs)

  • OTUs are clusters with sequence similarity and are accepted as an analytical unit used in microbial profiling using 16S rRNA gene markers.

Classification of Phylotype

  • A phylotype in microbiome research is a DNA sequence or group of sequences sharing more than an arbitrarily chosen level of similarity of a 16S rRNA gene marker.

Classification of Amplicon Sequence Variant (ASV)

  • An ASV in microbiome research is any one of the inferred single DNA sequences recovered from a bioinformatics analysis of 16S rRNA marker genes.

Classification of Microbiaal Phylogenies

  • Microbial phylogenies are estimated from gene sequences homologies and using models of mutation to infer most-likely evolutionary histories.






Mothur Microbiome Snakemake Workflow



Example of common FAQs (in progress)

  1. Mothur dist.seqs taking too long.
    • Length of the merged reads (merged reads over 300pb).
    • Not enough overlaping when merging the paired reads.
    • Use other pre-cluster algorithm like Deblur.
    • Too many uniques?
    • Not enough computer power?: Use HPC or Cluster.
    • Try to make contigs using maxee instead of deltaq or use phylogeny approach for downstream analysis, or use clister.split based on taxonomy.
    • do not forget to use controls.






References